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PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.

PerlPrimer's current features include the following:

- Calculation of possible primer-dimers- Retrieval of genomic or cDNA sequences from Ensembl (including both sequences automatically for QPCR)- Ability to BLAST search primers using the NCBI server or a local server- Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.- ORF and CpG island detection algorithms- Ability to add cloning sequences to primers, automatically adjusted to be in-frame- QPCR primer design without manual intron-exon boundary entry